Objective To study the changes of gene expression patterns in F1 hybrids of Chinese fir, analyze the transcriptomic profiling and to identify the associative genes related to heterosis, which presented a useful reference for the deep development and utilization of Chinese fir (Cunninghamia lanceolata).

Method Using the latest second-generation hybrids (Long 15×1339), HF1 (3 super-parent hybrids), LF2 (3 low-parent hybrids) and parents (P1 and P2), all sample groups were compared by transcriptome sequencing. Since Chinese fir transcriptome sequencing is lack of reference genome, so it is needed to do the sequencing reads first for de novo splice to get unigenes and transcripts. Subsequently, the functional annotation of transcripts, differential expression and other bioinformatic analysis approaches were adopted.

Result In a total of 12 samples, 5.8E+08 clean reads were generated by transcriptome sequencing, and the total length was 49 803 726 pb. BLASTX analysis is performed on clean reads in six databases (Nr, Swiss-prot, KOG, KEGG, Pfam, GO), through sequence alignment which results in 80 171 unigenes. The Venn diagram analysis revealed 5 transmission modes of DEGs from the parents to the progenies:1. parental expression but not expressed in hybrid (biparent silent type); 2. expression in one parent only, not in hybrids (parental specific expression); 3. only expressed in hybrids, not expressed in parents (hybrid specific expression); 4. expression in hybrid and one parent (single expression consistent); 5. expression in both parents and hybrids. 236 unigenes with differentially expressed (DEGs) were identified in HF1VSP1 comparison group, in HF1VSP2, LF2VSP1, and LF2VSP2, 1 483, 505, and 2 335DEGs were revealed respectively. 100 significant different unigenes among parents and progenies are screened out, and the heatmap clustering analysis was carried out. The results revealed the molecular mechanism of the heterosis of Chinese fir was over-dominant. The sizes of clustering block were different, indicating that some traits were controlled by oligogenes and some by polygenes. The superparental dominance of Chinese fir growth was determined by the 14 genes down-regulated in long15 and up-regulated in the superparent progeny.

Conclusion It is concluded that the molecular mechanisms of Chinese fir heterosis are over-dominant. The high productivity of Chinese fir superparental offsprings is related to 14 up-regulated genes. Environment significantly stimulates the up-regulated expression of these 14 genes, thus promotes the generation of growth advantages.